About a month ago I bought 2 pcs of Arduino DUE board from an Arduino distributor. After receiving the board, I found that the board is different from the official Eagle source file found on Arduino website. The board looks very good. But we still have some ideas to improve it. I began to think about build a compatible version. After a month, we made some process. I made an beta board, soldered by hand. Here is the changes we made from the official Arduino DUE:1. Remove the led on pin 13. Well, i fact I don't know exactly why I want to remove this led. Although this led will not affect the output of pin 13 on Arduino DUE now, I just want it to be simple. My feeling said, remove it. I hope you guys could give some suggestion.2. Remove the ATmega16U2. Since we could upload sketch from native USB now, I think the programming usb is not irreplacable any more. However, I breakout pins for external ATmega16u2 downloader (if any in the future). I think, many boards could share one downloader, like Arduino Mini. And the pins also make it possible for wireless downloaders. On some occasions, wires are annoying. I am thinking about the wireless downloader now.3. breakout all the unused pins. Maybe those pins will not be used in most cases. But i believe it will be used one day.4. breakout the Ethernet pins. I can see those pins on Arduino schematic. However, i guess due to limited space, finally the pins are gave up. Since i removed the ATmega16U2, there is space for those pins. Hopefully one day there will be ethernet library for those pins.There are also some small changes in the schematic. But they are not important.Here I need to collect new ideas to improve it further. Maybe several weeks later I will plan to sell those boards. But before that, anything else needs to be improved to Arduino DUE board?

Looks good. Since you have quite a bit of space left over, it would be useful if you add 3.3V <-> 5V support for shields, so that it's all-shield-ready out of the box, something that would obviously add significant value to your board. If you use a level translator like GTL2000 for this purpose, it would only add a dollar or two to the BOM cost.

There's a discussion going on about this over here: http://arduino.cc/forum/index.php/topic,136717.0.html